Enabled rendering of shapes with multiple holes (#506)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Tim Treis <[email protected]>

Author: 3 people

src/spatialdata_plot/pl/utils.py

@@ -1246,47 +1246,52 @@ def _get_linear_colormap(colors: list[str], background: str) -> list[LinearSegme
     return [LinearSegmentedColormap.from_list(c, [background, c], N=256) for c in colors]
 
 
-def _split_multipolygon_into_outer_and_inner(mp: shapely.MultiPolygon):  # type: ignore
-    # https://stackoverflow.com/a/21922058
-
-    for geom in mp.geoms:
-        if geom.geom_type == "MultiPolygon":
-            exterior_coords = []
-            interior_coords = []
-            for part in geom:
-                epc = _split_multipolygon_into_outer_and_inner(part)  # Recursive call
-                exterior_coords += epc["exterior_coords"]
-                interior_coords += epc["interior_coords"]
-        elif geom.geom_type == "Polygon":
-            exterior_coords = geom.exterior.coords[:]
-            interior_coords = []
-            for interior in geom.interiors:
-                interior_coords += interior.coords[:]
+def _collect_polygon_rings(
+    geom: shapely.Polygon | shapely.MultiPolygon,
+) -> list[tuple[np.ndarray, list[np.ndarray]]]:
+    """Collect exterior/interior coordinate rings from (Multi)Polygons."""
+    polygons: list[tuple[np.ndarray, list[np.ndarray]]] = []
+
+    def _collect(part: shapely.Polygon | shapely.MultiPolygon) -> None:
+        if part.geom_type == "Polygon":
+            exterior = np.asarray(part.exterior.coords)
+            interiors = [np.asarray(interior.coords) for interior in part.interiors]
+            polygons.append((exterior, interiors))
+        elif part.geom_type == "MultiPolygon":
+            for child in part.geoms:
+                _collect(child)
         else:
-            raise ValueError(f"Unhandled geometry type: {repr(geom.type)}")
+            raise ValueError(f"Unhandled geometry type: {repr(part.geom_type)}")
 
-    return interior_coords, exterior_coords
+    _collect(geom)
+    return polygons
+
+
+def _create_ring_codes(length: int) -> npt.NDArray[np.uint8]:
+    codes = np.full(length, mpath.Path.LINETO, dtype=mpath.Path.code_type)
+    codes[0] = mpath.Path.MOVETO
+    return codes
 
 
 def _make_patch_from_multipolygon(mp: shapely.MultiPolygon) -> mpatches.PathPatch:
     # https://matplotlib.org/stable/gallery/shapes_and_collections/donut.html
 
     patches = []
-    for geom in mp.geoms:
-        if len(geom.interiors) == 0:
-            # polygon has no holes
-            patches += [mpatches.Polygon(geom.exterior.coords, closed=True)]
-        else:
-            inside, outside = _split_multipolygon_into_outer_and_inner(mp)
-            if len(inside) > 0:
-                codes = np.ones(len(inside), dtype=mpath.Path.code_type) * mpath.Path.LINETO
-                codes[0] = mpath.Path.MOVETO
-                all_codes = np.concatenate((codes, codes))
-                vertices = np.concatenate((outside, inside[::-1]))
-            else:
-                all_codes = []
-                vertices = np.concatenate(outside)
-            patches += [mpatches.PathPatch(mpath.Path(vertices, all_codes))]
+    for exterior, interiors in _collect_polygon_rings(mp):
+        if len(interiors) == 0:
+            patches.append(mpatches.Polygon(exterior, closed=True))
+            continue
+
+        ring_vertices = [exterior]
+        ring_codes = [_create_ring_codes(len(exterior))]
+        for hole in interiors:
+            reversed_hole = hole[::-1]
+            ring_vertices.append(reversed_hole)
+            ring_codes.append(_create_ring_codes(len(reversed_hole)))
+
+        vertices = np.concatenate(ring_vertices)
+        all_codes = np.concatenate(ring_codes)
+        patches.append(mpatches.PathPatch(mpath.Path(vertices, all_codes)))
 
     return patches
 

tests/_images/Shapes_can_color_multipolygons_with_multiple_holes.png

@@ -99,6 +99,46 @@ def _make_multi():
         sdata["table"] = table
         sdata.pl.render_shapes(color="val", fill_alpha=0.3).pl.show()
 
+    def test_plot_can_render_multipolygons_with_multiple_holes(self):
+        square = [(0.0, 0.0), (5.0, 0.0), (5.0, 5.0), (0.0, 5.0), (0.0, 0.0)]
+        first_hole = [(1.0, 1.0), (2.0, 1.0), (2.0, 2.0), (1.0, 2.0), (1.0, 1.0)]
+        second_hole = [(3.0, 3.0), (4.0, 3.0), (4.0, 4.0), (3.0, 4.0), (3.0, 3.0)]
+        multipoly = MultiPolygon([Polygon(square, holes=[first_hole, second_hole])])
+        cell_polygon_table = gpd.GeoDataFrame(geometry=gpd.GeoSeries([multipoly]))
+        sd_polygons = ShapesModel.parse(cell_polygon_table)
+        sdata = SpatialData(shapes={"two_holes": sd_polygons})
+
+        fig, ax = plt.subplots()
+        sdata.pl.render_shapes(element="two_holes").pl.show(ax=ax)
+        ax.set_xlim(-1, 6)
+        ax.set_ylim(-1, 6)
+
+        fig.tight_layout()
+
+    def test_plot_can_color_multipolygons_with_multiple_holes(self):
+        square = [(0.0, 0.0), (5.0, 0.0), (5.0, 5.0), (0.0, 5.0), (0.0, 0.0)]
+        first_hole = [(1.0, 1.0), (2.0, 1.0), (2.0, 2.0), (1.0, 2.0), (1.0, 1.0)]
+        second_hole = [(3.0, 3.0), (4.0, 3.0), (4.0, 4.0), (3.0, 4.0), (3.0, 3.0)]
+        multipoly = MultiPolygon([Polygon(square, holes=[first_hole, second_hole])])
+        cell_polygon_table = gpd.GeoDataFrame(geometry=gpd.GeoSeries([multipoly]))
+        cell_polygon_table["instance_id"] = [0]
+        sd_polygons = ShapesModel.parse(cell_polygon_table)
+
+        adata = anndata.AnnData(pd.DataFrame({"value": [1]}))
+        adata.obs["region"] = pd.Categorical(["two_holes"] * adata.n_obs)
+        adata.obs["instance_id"] = [0]
+        adata.obs["category"] = ["holey"]
+        table = TableModel.parse(adata, region="two_holes", region_key="region", instance_key="instance_id")
+
+        sdata = SpatialData(shapes={"two_holes": sd_polygons}, tables={"table": table})
+
+        fig, ax = plt.subplots()
+        sdata.pl.render_shapes(element="two_holes", color="category", table_name="table").pl.show(ax=ax)
+        ax.set_xlim(-1, 6)
+        ax.set_ylim(-1, 6)
+
+        fig.tight_layout()
+
     def test_plot_can_color_from_geodataframe(self, sdata_blobs: SpatialData):
         blob = deepcopy(sdata_blobs)
         blob["table"].obs["region"] = pd.Categorical(["blobs_polygons"] * blob["table"].n_obs)